In cases like that, to be completely sure it's not a user app conflict, what I've done is break my user app restore into halves.
So I restore one half of the apps I want to, say maybe ones starting with A to M. If the problem doesn't occur try restoring half of the other half (a quarter), say N to T, etc, gradually narrowing down the offending app.
Once you restore a selection of apps and the problem occurs, then you'd have to restore a nandroid from before restoring any apps, then restore half of the apps that you did the last time. Just keep going and eventually you'll find the culprit. It might even make sense once you see which app is causing the problem.
Of course, another possibility is that the nightly is what has the conflict and that a newer nightly will fix it.
Sent from my Sprint Samsung Galaxy SIII on TouchWiz 4.4.2 with Wicked X v6.5, Ktoonsez' latest kernel and the latest Philz Touch Recovery.